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USGS-R / lakeReport

Scripts and report generator
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Lake Report

Scripts and report generator for Wisconsin Lake Reports.

Workflow

  1. Open RStudio & the lakeReport project
  2. Source the workflow-functions.R script
  3. Specify inputs to makeReports (see below)
  4. Run makeReports

Required Inputs for makeReports function

Input Type Description
siteNumber string value or vector the USGS station number OR auto
wy numeric value water year
plotNames string value or vector the name of the plot type you would like to produce [options: ghtable, stagehydrograph, qwtable, depthprofiles, qwtimeseries, auto]
output string value the format you would like the file saved as [options: pdf or word]

Optional Inputs for makeReports function with stagehydrograph

Input Type Description
filepath string value indicates where your csv is located
dateTime string value indicates the column name in your csv where dates are stored
gageHeight string value indicates the column name in your csv where gage heights are stored

Workflow Examples

More examples located in workflow-examples.R.

# single site, single report
wy <- 2014
siteNumber <- '05390500'
plotNames <- 'ghtable'
output <- 'pdf'
makeReports(siteNumber, wy, plotNames, output)

# single site, multiple reports as word
wy <- 2014
siteNumber <- '455638089034501'
plotNames <- c('qwtable', 'depthprofiles', 'qwtimeseries')
output <- 'word'
makeReports(siteNumber, wy, plotNames, output)

# get all plotNames from `plotNames_by_site.csv` for a single site
wy <- 2014
siteNumber <- '05390500'
plotNames <- 'auto'
output <- 'word'
makeReports(siteNumber, wy, plotNames, output)

# run all possible site and plotName combinations from `plotNames_by_site.csv`  
# currently makes all 89 combinations in ~ 6 minutes
wy <- 2014
siteNumber <- 'auto'
plotNames <- 'auto'
output <- 'word'
makeReports(siteNumber, wy, plotNames, output)

# use data from a file for stagehydrograph (not using dataRetrieval)
wy <- 2014
siteNumber <- '05390500'
plotNames <- 'stagehydrograph'
makeReports(siteNumber, wy, plotNames, 'pdf', 
            filePath = 'myfilepath',
            dateTime = 'sample_dt',
            gageHeight = 'result_va')

Dubgging

  1. Decide which plot/report type you are going to be debugging.
  2. Open workflow-functions.R, functions-[plotname].R, and [plotname].Rmd files.
  3. Source workflow-functions.R and functions-[plotname].R using the source button at the top right of your scripts window.
  4. Create the wy (numeric) and siteNumber (character) objects. You should debug using only one site at a time.
  5. Run all of the library() calls in the first chunk of [plotname].Rmd.
  6. You should now be able to step through each R chunk (greyed out box) of your [plotname].Rmd file.
  7. Should you come across a function that you would like to investigate, CTRL+Click the name of the function to navigate there. Then add browser() on the line you would like to stop. Save the file and source it again. Be careful with placing browser() inside if-else structures, unless you truly want to only pause when it meets that specific condition.
  8. Use the Next, Continue, and Stop buttons in the Console pane to navigate when in debug mode.
  9. Should you make any changes to the code, make sure to save and source the file. If you make changes to [plotname].Rmd, you will only need to save that file and rerun the lines of code.
  10. Before committing your changes, try running the overall report using makeReports and check that it looks as you would expect it to.

Committing Changes

New to this repo? Fork the master repository and setup remotes before trying to follow these directions.

  1. Always start by making sure your local code matches what is upstream (ideally, this would happen before you make changes to avoid any merge conflicts). Use git fetch upstream master and then git merge upstream/master to pull remote changes to your local repository.
  2. Use the "commit" button in your RStudio Git tab. Make sure you have checked the boxes of what you would like to commit. Then select "Commit". Type a message describing the changes, then click "Commit".
  3. Using the green up arrow, "push" your changes to your remote fork (online).
  4. Using a web browser, navigate to your remote fork.
  5. Select "New Pull Request", and then "Create Pull Request"
  6. Give your pull request (PR) a subject and a small description as necessary. If you are fixing a specific issue, reference that issue using # in the body of your PR. Then click "Create Pull Request".
  7. If you would like someone to review, call them out in a comment using @ or assign the PR to them. Otherwise, click "Merge".

Installing Packages

install.packages(c("dataRetrieval","dplyr","lubridate","gsplot", "knitr"))

Disclaimer

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy

Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.

This software is provided "AS IS."

CC0